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Djamaladdin G Musaev

Publications and source records attributed to Djamaladdin G Musaev.

At least 19 recordsLinked to original sources

Electronic reorganization: origin of sigma trans promotion effect.

Binding of two ligands trans to each other by some transition metal complexes may be cooperative [Khoroshun et al., Mol Phys 2002, 100, 523]. Several interesting consequent effects include (i) inverse relationship between bond strength and binding affinity; (ii) smaller coordination barriers to formation of weaker bonds; (iii) enhancement of Lewis acidity with increased number of ligands. We describe a simple model, sigma trans promotion effect (TPE), which considers electronic reorganization between two Lewis structures, and predicts the above-mentioned effects. The applied result of present study is the unified perspective on several facts of heme chemistry. Particularly, we reiterate an important but often overlooked notion, developed previously within the spin pairing model [Drago and Corden, Acc Chem Res 1980, 13, 353], that, in hemoproteins, the proximal histidine and the distal ligand such as O2 or CO cooperate in promoting electronic reorganization. As a result, depopulation of dz2 orbital upon ligand binding contributes to the phenomenon of hemoglobin cooperativity. The presented density functional (B3LYP) calculations on realistic models, the processes of carbon monoxide binding by Fe(II) porphyrins and dinitrogen binding by triamido/triamidoamine Mo(III) complexes, particularly the evaluation of the coordination barriers due to spin-state change by location of the minima on seams of crossing, support the TPE model predictions. From a broader theoretical perspective, the present study would hopefully stimulate the development of much needed frameworks and tools for facile comparisons of wave functions and their properties between different geometries, species, and electronic states. Advancement of practical wave function comparisons may yield fresh qualitative perspectives on chemical reactivity, and promote better understanding of related concepts such as electronic reorganization.

Journal Article↗

Does dinitrogen hydrogenation follow different mechanisms for [(eta5-C5Me4H)2Zr]2(mu2,eta2,eta2-N2) and {[PhP(CH2SiMe2NSiMe2CH2)PPh]Zr}2(mu2,eta2,eta2-N2) complexes? A computational study.

The mechanisms of dinitrogen hydrogenation by two different complexes--[(eta(5)-C(5)Me(4)H)(2)Zr](2)(mu(2),eta(2),eta(2)-N(2)), synthesized by Chirik and co-workers [Nature 2004, 427, 527], and {[P(2)N(2)]Zr}(2)(mu(2),eta(2),eta(2)-N(2)), where P(2)N(2) = PhP(CH(2)SiMe(2)NSiMe(2)CH(2))(2)PPh, synthesized by Fryzuk and co-workers [Science 1997, 275, 1445]--are compared with density functional theory calculations. The former complex is experimentally known to be capable of adding more than one H(2) molecule to the side-on coordinated N(2) molecule, while the latter does not add more than one H(2). We have shown that the observed difference in the reactivity of these dizirconium complexes is caused by the fact that the former ligand environment is more rigid than the latter. As a result, the addition of the first H(2) molecule leads to two different products: a non-H-bridged intermediate for the Chirik-type complex and a H-bridged intermediate for the Fryzuk-type complex. The non-H-bridged intermediate requires a smaller energy barrier for the second H(2) addition than the H-bridged intermediate. We have also examined the effect of different numbers of methyl substituents in [(eta(5)-C(5)Me(n)H(5)(-)(n))(2)Zr](2)(mu(2),eta(2),eta(2)-N(2)) for n = 0, 4, and 5 (n = 5 is hypothetical) and [(eta(5)-C(5)H(2)-1,2,4-Me(3))(eta(5)-C(5)Me(5))(2)Zr](2)(mu(2),eta(2),eta(2)-N(2)) and have shown that all complexes of this type would follow a similar H(2) addition mechanism. We have also performed an extensive analysis on the factors (side-on coordination of N(2) to two Zr centers, availability of the frontier orbitals with appropriate symmetry, and inflexibility of the catalyst ligand environment) that are required for successful hydrogenation of the coordinated dinitrogen.

Journal Article↗

The true nature of the Di-iron(III) gamma-Keggin structure in water: catalytic aerobic oxidation and chemistry of an unsymmetrical trimer.

The complex [gamma(1,2)-SiW(10){Fe(OH(2))}(2)O(38)](6)(-) (1) has been reported to catalyze the much sought reductant-free selective O(2)-based epoxidation of alkenes (Nishiyama, Y.; Nakagawa, Y.; Mizuno, N. Angew. Chem. Int. Ed. 2001, 40, 3639-3641) in chlorocarbon-acetonitrile solution. The challenge of reproducing catalysis by 1 led us to examine this chemistry in detail. In H(2)O, a desirable solvent for catalysis, 1, does not exist in the proposed organic-medium form in which the two iron atoms are in the binding pocket defined by the equatorial oxygens and, importantly, by two oxygens bound to the central Si heteroatom. Instead, 1 in H(2)O initially forms an unusual trimer [{Fe(2)(OH)(3)(H(2)O)(2)}(3)(gamma-SiW(10)O(36))(3)](15)(-) (2). The X-ray structure of 2 shows that the Fe-O(Si) bonds are cleaved and new bonds (mu-hydroxo bridges) form between these Fe centers and those of the neighboring [gamma(1,2)-SiW(10)Fe(2)] units. Structural, physical, and computational evidence indicate that if the bonds between the d-electron center, M (Fe in the case of 1 and 2), and the terminal ligands on M are stronger than the M-O(x)() bonds, then the out-of-pocket form is more stable and is the one observed. Significantly, 2 in H(2)O forms an intermediate that catalyzes the effective aerobic oxidation of sulfur compounds (mercaptoethanol is oxidized to the corresponding disulfide by O(2) at ambient pressure and temperature). All experimental findings are consistent with dissociation of a gamma-SiW(10) Keggin unit from the trimer, 2, to form the catalytically active species.

Journal Article↗

Is the protein surrounding the active site critical for hydrogen peroxide reduction by selenoprotein glutathione peroxidase? An ONIOM study.

In this ONIOM(QM:MM) study, we evaluate the role of the protein surroundings in the mechanism of H2O2 reduction catalyzed by the glutathione peroxidase enzyme, using the whole monomer (3113 atoms in 196 amino acid residues) as a model. A new optimization scheme that allows the full optimization of transition states for large systems has been utilized. It was found that in the presence of the surrounding protein the optimized active site structure bears a closer resemblance to the one in the X-ray structure than that without the surrounding protein. H2O2 reduction occurs through a two-step mechanism. In the first step, the selenolate anion (E-Se(-)) formation occurs with a barrier of 16.4 kcal/mol and is endothermic by 12.0 kcal/mol. The Gln83 residue plays the key role of the proton abstractor, which is in line with the experimental suggestion. In the second step, the O-O bond is cleaved, and selenenic acid (R-Se-OH) and a water molecule are formed. The calculated barrier for this process is 6.0 kcal/mol, and it is exothermic by 80.9 kcal/mol. The overall barrier of 18.0 kcal/mol for H2O2 reduction is in reasonable agreement with the experimentally measured barrier of 14.9 kcal/mol. The protein surroundings has been calculated to exert a net effect of only 0.70 kcal/mol (in comparison to the "active site only" model including solvent effects) on the overall barrier, which is most likely due to the active site being located at the enzyme surface.

Binding Sites↗

Insights into the mechanism of selective olefin epoxidation catalyzed by [gamma-(SiO4)W10O32H4]4-. A computational study.

A mechanism for the H2O2-based epoxidation of olefins catalyzed by the lacunary polyoxometalate (POM) [gamma-(SiO4)W10O32H4]4- (1) has been investigated at the DFT level. In this study, for the first time a "hydroperoxy" mechanism for this important process has been proposed. It is divided into two steps and investigated using the whole lacunary compound as a model. In the first step, a hydroperoxy (W-OOH) species and a water molecule are generated. The formation of this nonradical oxidant (W-OOH), consistent with the experimental suggestions, occurs with a barrier of 4.4 (7.2) kcal/mol (the number without parenthesis includes solvent effects in benzene, while the one with parenthesis is in the gas phase). In the second step, the O-O bond of the W-OOH species is cleaved, and an epoxide is formed. This step has a barrier of 38.7 (40.0) kcal/mol. It was found that the presence of one and two (CH3)4N+ countercations significantly reduces the rate-limiting barrier by 7.6 (8.3) and 11.9 (12.6) kcal/mol, respectively, and makes this lacunary POM a very efficient catalyst for epoxidation of olefins by hydrogen peroxide. It was demonstrated that the lacunary polyoxometalate basically acts as a mononuclear W(VI) complex in activating the oxidant, a conceptually noteworthy finding.

Journal Article↗

Computational studies of nucleophilic attack and protonation of electron-deficient benzoheterocycle triosmium clusters.

The density functional theory method has been applied to gain insights into the regioselectivity of nucleophilic attack and protonation of electron-deficient benzoheterocycle triosmium clusters. We report our computational results on the reaction of the green 46-electron triosmium clusters Os3(CO)(9)(mu3-eta2-(LH))(mu-H) (L = benzoxazole, 1a; benzothiazole, 1b; dihydroquinoline, 1c; 1,3-dehydroindoline, 1d; 4H-3,1-benzoxazine, 1e) with hydride (H-) and proton (H+) in order to elucidate factors affecting the observed differences in the structure of the kinetic products of these reactions. Transition-state calculations for the interconversion of the anionic tautomers resulting from H- attack on the clusters 1a-e show that the activation energies of these anionic clusters are considerably lower than the previously reported barriers for related neutral clusters. Calculations also reveal that the structures of the kinetic products resulting from sequential H-/H+ attack are determined by the protonation process.

Journal Article↗

Peroxynitrite reductase activity of selenoprotein glutathione peroxidase: a computational study.

The peroxynitrite reductase activity of selenoprotein glutathione peroxidase (GPx) has been investigated using density functional theory calculations for peroxynitrite/peroxynitrous acid (ONOO-/ONOOH) substrates through two different "oxidation" and "nitration" pathways. In the oxidation pathway for ONOO-, the oxidation of GPx and the subsequent formation of the selenenic acid (E-Se-OH) occur through a concerted mechanism with an energy barrier of 4.7 (3.7) kcal/mol, which is in good agreement with the computed value of 7.1 kcal/mol for the drug ebselen and the experimentally measured barrier of 8.8 kcal/mol for both ebselen and GPx. For ONOOH, the formation of the E-Se-OH prefers a stepwise mechanism with an overall barrier of 6.9 (11.3) kcal/mol, which is 10.2 (11.2) kcal/mol lower than that for hydrogen peroxide (H2O2), indicating that ONOOH is a more efficient substrate for GPx oxidation. It has been demonstrated that the active site Gln83 residue plays a critical role during the oxidation process, which is consistent with the experimental suggestions. The nitration of GPx by ONOOH produces a nitro (E-Se-NO2) product via either of two different mechanisms, isomerization and direct, having almost the same barrier heights. A comparison between the rate-determining barriers of the oxidation and nitration pathways suggests that the oxidation of GPx by ONOOH is more preferable than its nitration. It was also shown that the rate-determining barriers remain the same, 21.5 (25.5) kcal/mol, in the peroxynitrite reductase and peroxidase activities of GPx.

Computational Biology↗

Density functional study of the roles of chemical composition of di-transition-metal-substituted gamma-Keggin polyoxometalate anions.

The roles of chemical composition (X, M and M(FW)) of di-transition-metal-substituted gamma-Keggin polytungstates and polymolybdates, [(X(n)(+)O(4))M(2)(OH)(2)(M(FW))(10)O(32)]((8-n)-), on the geometry, electronic structure, and magnetic properties of these species have been investigated at the density functional level. It was shown that the change of the heteroatom X via Al(III)-Si(IV)-P(V)-S(VI) slightly stabilizes the broken-symmetry (BS) state over the high-spin (HS) state, increases the antiferromagnetic coupling constant, J, of these species, and lowers the energies of their highest-occupied molecular orbitals (HOMOs) and lowest-unoccupied molecular orbitals (LUMOs). The change of the redox-active center M from Mn to Fe slightly increases the M-(XO(4)) interaction, J-coupling constant, and energy gap between the HS and BS states. Meanwhile, the LUMOs are stabilized, indicating the stronger oxidant character of [(X(n)(+)O(4))M(2)(OH)(2)W(10)O(32)]((8-n)-) for M = Fe than Mn. It was shown that the change of addenda atom M(FW) from W to Mo makes (a) the geometry of Keggin "cage" slightly smaller, (b) the interaction of redox-active centers (Fe) with the central XO(4)-unit slightly stronger, and (c) the J-coupling constant, as well as the energy gap DeltaE(BS-HS), slightly larger.

Journal Article↗

Computational insights into the mechanism of radical generation in B12-dependent methylmalonyl-CoA mutase.

ONIOM calculations have provided novel insights into the mechanism of homolytic Co-C5' bond cleavage in the 5'-deoxyadenosylcobalamin cofactor catalyzed by methylmalonyl-CoA mutase. We have shown that it is a stepwise process in which conformational changes in the 5'-deoxyadenosine moiety precede the actual homolysis step. In the transition state structure for homolysis, the Co-C5' bond elongates by approximately 0.5 Angstroms from the value found in the substrate-bound reactant complex. The overall barrier to homolysis is approximately 10 kcal/mol, and the radical products are approximately 2.5 kcal/mol less stable than the initial ternary complex of enzyme, substrate, and cofactor. The movement of the deoxyadenosine moiety during the homolysis step positions the resulting 5'-deoxyadenosyl radical for the subsequent hydrogen atom transfer from the substrate, methylmalonyl-CoA.

Adenosine↗

The role of the central atom in structure and reactivity of polyoxometalates with adjacent d-electron metal sites. computational and experimental studies of gamma-[(Xn+O4)RuIII2(OH)2(MFM)10O32](8-n)-) for MFM = Mo and W, and X = AlIII, SiIV, PV, and SVI.

The role of the central atom X in the structure and reactivity of di-Ru-substituted gamma-Keggin polyoxometalates (POMs), gamma-[(Xn+O4)RuIII2(OH)2(MFM)10O32](8-n)-), where MFM = Mo and W, and X = AlIII, SiIV, PV, and SVI., was computationally investigated. It was shown that for both MFM = Mo and W the nature of X is crucial in determining the lower lying electronic states of the polyoxoanions, which in turn likely significantly impacts their reactivity. For the electropositive X = AlIII, the ground state is a low-spin state, while for the more electronegative X = SVI the ground state is a high-spin state. In other words, the heteroatom X can be an "internal switch" for defining the ground electronic states of the gamma-M2-Keggin POMs. The obtained trends, in general, are less pronounced for MFM = Mo than for W. On the basis of the comparison of the calculated energy gaps between low-spin and high-spin states of polytungstates and polymolybdates, we predict that the gamma-M2-Keggin polytungstates could be more reactive than their polymolybdate analogues. For purposes of experimental verification the computationally predicted and evaluated polytungstate gamma-[(SiO4)RuIII2(OH)2(OH2)2W10O32]4- was prepared and characterized.

Journal Article↗

A DFT study of the mechanism of Ni superoxide dismutase (NiSOD): role of the active site cysteine-6 residue in the oxidative half-reaction.

In the present DFT study, the catalytic mechanism of H2O2 formation in the oxidative half-reaction of NiSOD, E-Ni(II) + O2- + 2H+ --> E-Ni(III) + H2O2, has been investigated. The main objective of this study is to investigate the source of two protons required in this half-reaction. The proposed mechanism consists of two steps: superoxide coordination and H2O2 formation. The effect of protonation of Cys6 and the proton donating roles of side chains (S) and backbones (B) of His1, Asp3, Cys6, and Tyr9 residues in these two steps have been studied in detail. For protonated Cys6, superoxide binding generates a Ni(III)-O2H species in a process that is exothermic by 17.4 kcal/mol (in protein environment using the continuum model). From the Ni(III)-O2H species, H2O2 formation occurs through a proton donation by His1 via Tyr9, which relative to the resting position of the enzyme is exothermic by 4.9 kcal/mol. In this pathway, a proton donating role of His1 residue is proposed. However, for unprotonated Cys6, a Ni(II)-O2- species is generated in a process that is exothermic by 11.3 kcal/mol. From the Ni(II)-O2- species, the only feasible pathway for H2O2 formation is through donation of protons by the Tyr9(S)-Asp3(S) pair. The results discussed in this study elucidate the role of the active site residues in the catalytic cycle and provide intricate details of the complex functioning of this enzyme.

Amino Acid Sequence↗

Elucidation of the mechanism of selenoprotein glutathione peroxidase (GPx)-catalyzed hydrogen peroxide reduction by two glutathione molecules: a density functional study.

The mechanism of the hydrogen peroxide reduction by two molecules of glutathione catalyzed by the selenoprotein glutatione peroxidase (GPx) has been computationally studied. It has been shown that the first elementary reaction of this process, (E-SeH) + H(2)O(2) --> (E-SeOH) + H(2)O (1), proceeds via a stepwise pathway with the overall barrier of 17.1 kcal/mol, which is in good agreement with the experimental barrier of 14.9 kcal/mol. During reaction 1, the Gln83 residue has been found to play a key role as a proton acceptor, which is consistent with experiments. The second elementary reaction, (E-SeOH) + GSH --> (E-Se-SG) + HOH (2), proceeds with the barrier of 17.9 kcal/mol. The last elementary reaction, (E-Se-SG) + GSH --> (E-SeH) + GS-SG (3), is initiated with the coordination of the second glutathione molecule. The calculations clearly suggest that the amide backbone of the Gly50 residue directly participates in this reaction and the presence of two water molecules is absolutely vital for the reaction to occur. This reaction proceeds with the barrier of 21.5 kcal/mol and is suggested to be a rate-determining step of the entire GPx-catalyzed reaction H(2)O(2) + 2GSH --> GS-SG + 2H(2)O. The results discussed in the present study provide intricate details of every step of the catalytic mechanism of the GPx enzyme and are in good general agreement with experimental findings and suggestions.

Catalysis↗

A palladium-oxo complex. Stabilization of this proposed catalytic intermediate by an encapsulating polytungstate ligand.

A terminal Pd-oxo unit is reported. The unit is encapsulated in a cavity defined by two [A-alpha-PW9O34]9- units fused together by one [WO(OH2)]4+ center and forms from Pd(II) in buffered media in the presence of O2. Both X-ray diffraction and EXAFS data are consistent with a Pd-oxo bond distance of ca. 1.65 A. 17O NMR studies confirm that the solid-state structure is maintained in solution.

Catalysis↗

Density Functional Study of Mo-Carbonyl-Catalyzed Alkynol Cycloisomerization: Comparison with W-Catalyzed Reaction.

Mo-catalyzed endo-cycloisomerizations of alkynes tethered to alcohols have been studied using density functional theory, and comparisons were made with the W-catalyzed reaction. The cycloisomerization is initiated with the formation of metal alkyne pi complex and is followed by the rate-determining step, which transforms the pi complex to a vinylidene carbene complex, considered to be critical for endo-mode cyclization. Several different alkynols have been selected to investigate five- and six-membered ring endo-cycloisomerizations in the presence of Mo(CO)(5) catalyst. The energy barriers calculated for five- and six-membered ring cycloisomerizations are within a range of 25-30 kcal/mol for most cases studied, showing no significant energy difference between the two metals. The stabilization effect of THF and Et(3)N solvents and the substitution reaction of THF by alkynol substrates in the reaction process with Mo and W complexes are studied as well. The principal difference between Mo- and W-catalyzed cycloisomerization processes appears to be the initial formation of a pi complex, which is more stabilizing for formation of the W-alkyne vs Mo-alkyne complexes.

Journal Article↗

Metal-peroxo versus metal-oxo oxidants in non-heme iron-catalyzed olefin oxidations: computational and experimental studies on the effect of water.

Computational and experimental studies show that Fe(BPMEN)-catalyzed olefin oxidation has two (FeIII-OOH and FeV=O) oxidant species, which act with comparable activation barriers. The presence of water favors formation of an HO-FeV=O oxidant via water-assisted O-OH bond cleavage and leads to both epoxide and cis-diol products. In the absence of water, the oxidant is the FeIII-OOH [or (MeCN)FeIII-OOH], and oxidation mainly leads to epoxide. This conclusion differs from that derived from DFT investigations of iron-porphyrin-catalyzed olefin epoxidation, where the FeIII-OOH pathway is deemed too high in energy to be plausible. The difference between these two systems may lie in the more flexible coordination environment of the non-heme iron complex, which has an available adjacent coordination site that contributes to the activation of the peroxide in both wa and nwa pathways.

Alkenes↗

Asymmetric terminal ligation on substituted sites in a disorder-free Keggin anion, [beta-SiFe2W10O36(OH)2(H2O)Cl]5-.

A new monomeric diiron beta-Keggin derivative, [(CH3)2NH2]5[beta-SiFe2W10O36(OH)2(H2O)Cl].7H2O (1) with non-adjacent substituted sites has been obtained in good yield by reaction of Fe(III) cations with [gamma-SiW10O36]8- in aqueous solution. The use of hydrogen bonding counter-cations produced a disorder-free polyanion. This situation facilitates unequivocal identification of the terminal ligands on Fe atoms and interpretation of the magnetic properties, which are also addressed by DFT calculations. Electrochemical studies establish that 1 can be step-wise reduced by two electrons and then reversibly oxidized.

Journal Article↗

A comparative study of various computational approaches in calculating the structure of pyridoxal 5'-phosphate (PLP)-dependent beta-lyase protein. The importance of protein environment.

Various computational approaches, using molecular mechanics (Amber), semiempirical (AM1), density functional (B3LYP), and various ONIOM methods, have been comparatively investigated for the structure of Escherichia coli NifS CsdB protein. The structure of the entire monomer containing 407 amino acid residues and 579 surrounding water molecules has been optimized. The full geometry optimization in the "active site-only" approach (including only active site atoms) has been found to give the largest root-mean-square (RMS) deviation from the X-ray structure; a much better agreement has been achieved by keeping the atoms leading to the backbones of some amino acids frozen in their positions in the X-ray structure. The best agreement has been attained by including the surrounding protein in the calculations using the two-layer ONIOM (B3LYP:Amber) approach. The results presented in this study conclusively demonstrate the importance of the protein/active-site interaction on the active-site structure of the enzyme. The present theoretical study represents the largest system studied at the ONIOM level to date, containing 7992 atoms, including 84 atoms in the QM region and rest in the MM region.

Binding Sites↗